Protesters, opposing Egyptian President Mohamed Mursi, wave the Egyptian flag and shout slogans against him and members of the Muslim Brotherhood at the Brotherhood's headquarters in Cairo's Moqattam district July 1, 2013. (AMR ABDALLAH DALSH/REUTERS)

Protesters, opposing Egyptian President Mohamed Mursi, wave the Egyptian flag and shout slogans against him and members of the Muslim Brotherhood at the Brotherhood's headquarters in Cairo's Moqattam district July 1, 2013.(AMR ABDALLAH DALSH/REUTERS)

Families had stockpiled food and water, drivers had slept nights in petrol lines that snaked for city block after city block, and half a dozen people had died in a days-long spasm of violence that exploded into a full-blown seizure on Sunday, when mass protests against President Mohamed Morsi broke out and brought out the largest crowds in Egypt’s modern history. The headquarters of the Mr. Morsi's Muslim Brotherhood were set on fire on Sunday night, after offices of the Brotherhood’s ruling Freedom and Justice Party were attacked and burned throughout the Nile Delta. Brotherhood toughs have banded together outside their offices wearing hard hats and makeshift shields and carrying homemade guns, ready to bludgeon or blow away what they fear is the very embodiment of the counter-revolution.

One online commentator described the mass movement to oust Mr. Morsi on the anniversary of his election – a movement known as Tamarod (“rebel”) – as the birth of a new political order that may kill its mother. A journalist said it was as if Egypt’s body politic were rejecting a transplant and killing the nation in the process, a fledgling democracy’s auto-immune system gone haywire.

How did the country get here? How did the January 2011 uprising and its young, made-for-TV activists spin out into another zero-sum game for control? The story is complicated, and the strategic and tactical failures by both the secularist opposition and the Muslim Brotherhood are so profoundly, majestically short-sighted and self-defeating that some have retreated into that most time-tested of rationales, the conspiracy, to explain how things could have gone so wrong, so fast. In their narrative, the crisis has been stage-managed by the military, Egypt’s eminence grise and ultimate power-broker, beginning on the day in February 2011 when the generals opportunistically seized on the mass protests to quietly but forcefully escort President Hosni Mubarak, his family and his cronies from the stage.

Like most conspiracy theories, the story has a seed of truth. In the heady days before and after the fall of Mr. Mubarak, the generals were taking everyone’s temperature. At one time or another, they chatted with many of the revolution’s most prominent instigators. They met with Ahmed Maher of the April 6th Movement. They met with representatives of the Brotherhood. Mohamed Aboul Ghar, who would soon found one of the only serious non-Islamist political parties in the country, once told me how he, the editor of Al Ahram newspaper, and two other men were called before five generals that March. One kept notes as they spoke; he was Abdelfattah el-Sisi, later promoted to defence minister and military commander-in-chief under Mr. Morsi. As the meeting adjourned, one of the generals casually remarked that the Supreme Council of the Armed Forces -- the military’s governing body -- had in 2010 held a meeting without Mr. Mubarak, their commander, and decided not to allow the president’s son, Gamal, to complete a widely telegraphed succession during rigged presidential elections then scheduled for 2011.

“The plan [was], when Gamal is going to take over, they are going make a coup,” Aboul Ghar recalled. The military’s disdain for Gamal and his generation of casually corrupt businessmen was well known, as was their desire not to see him crowned, and the January uprising provided a perfect opportunity to abort the Mubarak family dynasty. But after it became obvious that the masses would not accept a handover to Omar Suleiman, Mr. Mubarak’s last-minute vice president and intelligence chief, the military needed a placeholder. Picking out a suitable figure from Mr. Mubarak’s old National Democratic Party network would be impossible -- not in the aftermath of a rebellion that left their headquarters smoldering, their party dissolved, and their leaders facing prosecution. Egypt’s political opposition, meanwhile, had been carefully neutered and co-opted for five decades; it had no base and its leaders no respect on the streets.

The only suitable dancing partner was the Muslim Brotherhood, an institution whose organizational, bureaucratic and service-providing experience was deeper than even that of the post-1956 militarized government itself.

And so the transition proceeded under military rule, directed by old, conservative men who learned their craft in a much different Egypt, half of them hoping to protect the old order, the other half pushing their project to usher in a new one. A temporary constitution orchestrated by the military and backed by the Brotherhood and their ultraconservative allies passed easily. Calls from figures such as Mohamed ElBaradei to create a liberal, progressive and inclusive new constitution from scratch, written by an independent body chosen by consensus, were ignored. As the year dragged on, poor Egyptians remained poor, and Mr. Mubarak sat uncharged with any crime in a military hospital. Protests against the military’s reluctance to hand over power grew. They were supported by the Brotherhood, which likely saw in the unrest a useful tactic to keep their prime opponent on the back foot. In November 2011, the protests threatened to get out of control.

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